Plot hole: When Blair walks into Chazz's dorm, Hassleberry says "It's Blair" as if he knows her. However, Hassleberry has never met Blair and shouldn't know who she is. (00:19:15)
Inter-Dimension Detention - S3-E16
Plot hole: When the Harpy monster begins carrying Crowler and Bonaparte, Jesse has his Sapphire Pegasus attack it. Once it is attacked, the monster drops Crowler and Bonaparte, but the monster is never seen landing on the ground, or anywhere for the rest of the scene. (00:04:58)
Plot hole: When Marcel is standing in an abandoned area, he hears Bonaparte shout his name. Adrian is then seen standing a short distance behind Marcel, and then hides once he sees Bonaparte approaching. There's no way Bonaparte didn't see Adrian. Even if Adrian hid, Bonaparte was already close enough to see Marcel, so he should have seen Adrian as well, or at the very least, seen him on his way to find Marcel. (00:17:10)
Return of the Sacred Beasts - S3-E22
Plot hole: When Marcel is running through the underground chasm, Chazz emerges from a small passageway that Marcel passes. The last time Chazz was seen, he was one of the Duel Ghouls approaching Jaden at the end of the previous episode. Marcel only got to where he was so quickly because jumped and ran through a chasm he opened, so there's no way Chazz could have gotten down there through a hidden passageway before him. (00:03:35)
The Power Within: Part 2 - S3-E48
Plot hole: Jaden activates Super Polymerization to fuse Elemental Hero Neos and Rainbow Dark Dragon to summon Rainbow Neos. Where exactly did Rainbow Neos come from? All the cards used in the Yu-Gi-Oh universe come from companies that developed them and the Rainbow Dragon card was only first made earlier in the season, so there's no way a monster that requires Rainbow Dragon as a Fusion material monster would exist. (00:17:43 - 00:18:43)
